Showing : proteomics • reset
2
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111
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Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 18 days ago by 60k • written 18 days ago by • 0
0
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0
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44
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Questions about msqrob2: raw vs LFQ intensities, model design with blocking
msqrob2 ProteomicsWorkflow proteomics
22 days ago Jane • 0
1
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0
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95
views
Job: PhD Positions in Computational Research, Data Science and Artificial Intelligence at the German Cancer Research Center (DKFZ)
phd cancer genomics proteomics bioinformatics
5 weeks ago DKFZ International PhD Program ▴ 10
0
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0
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79
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ProteoMM analysis with two replicates
shotgunproteomics Proteome proteomics Proteomics ProteoMM
11 weeks ago ary.lech ▴ 10
0
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2
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272
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Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 3 months ago by 45k • written 3 months ago by • 0
0
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0
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152
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Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
4 months ago Robert Castelo ★ 2.9k
0
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1
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336
views
limma/voom for protein intensity data
limma proteomics voom
updated 8 months ago by ★ 1.2k • written 8 months ago by ▴ 60
0
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1
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212
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How to pull-down gene/protein names from the database search, using R ?
proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics
updated 9 months ago by 45k • written 9 months ago by • 0
0
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5
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340
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In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 9 months ago by 45k • written 9 months ago by • 0
0
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0
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186
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How to handle the imputation and normalisation?
Proteomics DEP limma
9 months ago barrypraveen • 0
0
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1
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270
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How to remove batch effect on DEP protemics package?
Proteomics DEP MassSpectrometryData
updated 10 months ago by • 0 • written 10 months ago by • 0
0
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0
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449
views
what is the difference between iBAQ or LFQ?
Proteomics DEP limma
10 months ago barrypraveen • 0
0
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4
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362
views
How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
11 months ago barrypraveen • 0
4
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3
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997
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Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 14 months ago by 45k • written 14 months ago by ▴ 10
6
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6
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631
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 14 months ago by 45k • written 14 months ago by ▴ 10
0
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0
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367
views
Limma design multi-level experiment with 3 time points
R proteomics limma
14 months ago ellen2270 • 0
0
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4
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380
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DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
14 months ago rina ▴ 20
0
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0
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372
views
Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
15 months ago Robert Castelo ★ 2.9k
2
votes
1
reply
1.1k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 16 months ago by 60k • written 16 months ago by ★ 1.5k
0
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0
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447
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Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
17 months ago Laura • 0
1
vote
2
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397
views
calculate theoretical isotope distribution give the AA sequence
Metabolomics proteomics MassSpectrometry
17 months ago Oliver • 0
0
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3
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392
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Why I can not install rTANDEM?
MassSpectrometry Proteomics mzR
17 months ago Gilad • 0
1
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2
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399
views
error in installation of 'org.Hs.eg.db'
proteomics GenomicSequence
updated 18 months ago by ▴ 70 • written 18 months ago by • 0
5
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6
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665
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possible package naming conflict
proteomics
18 months ago Tobias ▴ 30
1
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0
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423
views
News: Online training - Proteomics in R and Bioconductor
ProteomicsWorkflow proteomics Proteome
18 months ago info ▴ 10
0
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0
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228
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Which software can work withThermo ProteomeDiscover software output?
ProteomicsWorkflow proteomics proteinProfiles
18 months ago yueli7 ▴ 10
0
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1
reply
385
views
R package to change protein *.msf file to any readable file
Proteome ProteomicsWorkflow proteomics
updated 18 months ago by ★ 1.0k • written 18 months ago by ▴ 10
0
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0
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380
views
Job: Data Scientist Proteomics (100%), Biozentrum, University of Basel, Switzerland
Switzerland JobPosting Basel Proteomics
18 months ago Robert Ivanek ▴ 730
0
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3
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552
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Find DEPs among TMT labeling proteom time course data by limma
limma proteomics TMTlabeling timecoursedata
updated 18 months ago by ▴ 270 • written 19 months ago by • 0
3
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0
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905
views
Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
19 months ago Johannes Rainer ★ 1.9k
2
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0
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393
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Job: PostDoc position for the analysis of large scale metabolomics data
metabolomics proteomics Job
20 months ago Johannes Rainer ★ 1.9k
1
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6
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1.3k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 22 months ago by 1.5k • written 22 months ago by • 0
0
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0
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641
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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
software engineer RNASeq proteomics Job visualisation
23 months ago Laurent Gatto 1.5k
0
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0
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226
views
How to generate custom MS database using CustomProDB?
r proteomics
2.1 years ago nattzy94 ▴ 20
2
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1
reply
382
views
Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
2.2 years ago daniel.magnus.bader ▴ 40
2
votes
1
reply
375
views
Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
2.2 years ago harelarik ▴ 50
1
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0
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433
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
2.3 years ago Laurent Gatto 1.5k
1
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2
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950
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
2.4 years ago Rob • 0
0
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0
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405
views
Job: Bioinformatician Positions at the University of Chicago BSD Bioinformatics Core
RNA-seq DNA-seq ATAC-seq proteomics microbiome Job
2.4 years ago lhuang7 ▴ 50
3
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0
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1.6k
views
Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
2.6 years ago • updated 2.4 years ago Gordon Smyth 45k
0
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0
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637
views
News: May Institute Computation and statistics for mass spectrometry and proteomics
conference mass spectrometry proteomics News
2.4 years ago shepherl 3.1k
0
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0
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490
views
News: course - Protemics with R and Bioconductor - 17-19 February 2020 in Berlin
Bioconductor R Proteomics News
2.5 years ago info ▴ 10
0
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0
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269
views
proteoQC throwing error after running
ProteoQC Proteomics
2.5 years ago laural710 • 0
0
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2
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696
views
Total Area Sum Intensity based Normalization for label-free quantitative proteomics
normalization proteomics label-free
2.6 years ago amolares • 0
0
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3
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730
views
Writing a loop through multiple fasta files and named files (is it possible with MSGFplus?)
MSGF+ Proteomics r
updated 2.6 years ago by 25k • written 2.6 years ago by • 0
0
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0
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302
views
DEP package - Understanding the results table
dep proteomics logFC
2.6 years ago rina ▴ 20
0
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0
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424
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DEP: TMT analysis from MaxQuant output
DEP TMT proteomics
2.7 years ago dparrine • 0
2
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0
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1.8k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
2.7 years ago Laurent Gatto 1.5k
0
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0
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332
views
News: Protemics with R and Bioconductor course in Berlin
R Proteomics News
2.7 years ago info ▴ 10
0
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0
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430
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Proteomics data analysis with DEP no replicates
DEP Proteomics Statistics limma
2.8 years ago tatabox • 0
50 results • Page 1 of 1
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Comment: Italicise by Pau • 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa by priyanka.m • 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values by wahaha • 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Comment: DESeq2 how to specify contrast to test difference of differences by Nicole • 0
Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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